Contacts of the helix formed by residues 348 - 353 (chain A) in PDB entry 1PTH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.6 33.4 - + - -
201A PHE* 3.5 35.2 - + + -
202A ALA* 3.0 34.7 - - + +
205A PHE* 5.0 6.2 - + - -
206A THR* 4.7 1.2 - - - +
343A ILE 3.0 10.8 + - - +
344A VAL* 3.0 24.7 - - + +
347A GLU* 1.3 78.8 - - - +
349A VAL* 1.3 78.6 + - + +
351A GLN* 3.0 3.2 + - - +
352A LEU* 3.0 29.7 + - + +
385A TYR* 3.0 31.7 + - - -
387A TRP* 3.8 1.7 - - - -
530A 0AH 4.9 2.5 - - - -
580A PHE* 3.7 16.7 - + + -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A VAL* 2.7 29.5 + - + +
345A ILE* 3.5 14.8 + - + +
348A TYR* 1.3 85.3 - - + +
350A GLN* 1.3 62.9 + - - +
352A LEU* 3.9 5.3 - - + +
353A SER* 2.9 22.4 + - - -
359A LEU* 3.4 16.4 - - + -
530A 0AH 4.9 8.7 - - - +
531A LEU* 5.2 6.1 - - + -
534A LEU* 5.1 5.4 - - + -
710A SAL 3.0 48.0 - - + +
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Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ILE 3.5 4.8 + - - +
346A GLU 3.2 27.2 - - - +
347A GLU* 3.3 4.7 - - - +
348A TYR 3.1 0.4 - - - -
349A VAL* 1.3 77.5 - - - +
351A GLN* 1.3 54.4 + - - +
353A SER* 2.9 5.9 + - - -
354A GLY* 2.8 32.6 + - - -
355A TYR* 3.1 29.4 + - - +
356A PHE 4.9 0.2 - - - -
357A LEU 2.9 22.7 + - - -
358A GLN* 3.6 8.6 - - - +
359A LEU* 2.7 38.9 + - - +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.8 19.1 + - - +
193A GLY 3.7 4.8 + - - -
194A THR* 3.1 53.5 + - + +
198A PHE* 4.2 4.9 - - + -
347A GLU 3.0 9.4 + - - +
348A TYR 3.4 7.9 - - - +
350A GLN* 1.3 79.6 - - - +
352A LEU* 1.3 66.7 + - - +
353A SER 3.1 1.0 + - - -
354A GLY* 3.3 11.3 + - - -
580A PHE* 3.7 29.8 + - + -
581A HIS* 3.9 19.0 - - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLN* 3.1 17.4 + - - +
194A THR* 5.8 2.0 - - + -
198A PHE* 3.6 28.5 - - + -
348A TYR* 3.0 17.1 + - + +
349A VAL* 3.9 6.5 - - - +
351A GLN* 1.3 82.0 - - - +
353A SER* 1.3 57.0 + - - +
387A TRP* 3.6 25.8 - - + -
517A ILE* 3.8 23.0 - - + +
518A PHE* 3.6 34.9 - - + -
523A ILE* 5.8 0.3 - - - +
530A 0AH 4.0 4.5 - - + -
710A SAL 3.8 28.0 - - + -
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A HIS* 4.1 12.2 + - - -
94A THR* 4.7 0.9 - - - +
192A GLN* 4.0 5.8 + - - -
349A VAL* 2.9 17.5 + - - -
350A GLN* 3.1 10.2 + - - -
352A LEU* 1.3 79.1 - - - +
354A GLY* 1.3 61.2 + - - +
355A TYR* 3.0 57.8 + - - +
359A LEU* 4.4 2.1 - - - +
523A ILE* 5.7 3.8 - - - +
710A SAL 4.5 19.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il